5-25760570-G-T

Variant names:

• chr5-25760570-G-T
• rs7727656
• ENST00000738207.1:n.163+15188G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000738207.1(ENSG00000296327):​n.163+15188G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,062 control chromosomes in the GnomAD database, including 32,703 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (32703 hom., cov: 33)
• Consequence: ENSG00000296327 ENST00000738207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 8 publications found

Genes affected

ENSG00000296327 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296327	ENST00000738207.1	n.163+15188G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96096 AN: 151944 Hom.: 32691 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.644

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.632 AC: 96130 AN: 152062 Hom.: 32703 Cov.: 33 AF XY: 0.628 AC XY: 46691 AN XY: 74332

African (AFR) AF: 0.377 AC: 15628 AN: 41456

American (AMR) AF: 0.669 AC: 10228 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2735 AN: 3466

East Asian (EAS) AF: 0.509 AC: 2627 AN: 5160

South Asian (SAS) AF: 0.684 AC: 3295 AN: 4820

European-Finnish (FIN) AF: 0.638 AC: 6746 AN: 10570

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52478 AN: 67994

Other (OTH) AF: 0.647 AC: 1366 AN: 2112

Alfa AF: 0.721 Hom.: 143491

Bravo AF: 0.620

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.66
PhyloP100		-0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7727656; hg19: chr5-25760679;